Gene Network Explorer (GeneEx)
GeneEx is an interactive web-app that employs an ODE-based mathematical modeling approach to simulate, visualize, and analyze gene regulatory circuits (GRCs) for an explicit kinetic parameter set or for a large ensemble of
random parameter sets. GeneEx offers users the freedom to modify many aspects of the simulation such as the parameter ranges, the levels of gene expression noise, and the GRC network topology itself. This degree of flexibility allows users to explore a variety of hypotheses by providing insight into the number and stability of attractors for a given GRC. Moreover, users have the option to upload, and subsequently compare, experimental gene expression data to simulated data generated from the analysis of a built or uploaded custom circuit. Finally, GeneEx offers a curated database that contains circuit motifs and known biological GRCs to facilitate further inquiry into these. Overall, GeneEx enables users to investigate the effects of parameter variation, stochasticity, and/or topological changes on gene expression for GRCs using a systems-biology approach.
Reference:
V. Kohar, D. Gordin, A. Ketabi and M. Lu, Gene Circuit Explorer (GeneEx): an interactive web-app and database for visualizing, simulating and analyzing gene regulatory circuits. (in revision)
V. Kohar and M. Lu. (2018) Role of noise and parametric variation in the dynamics of gene regulatory circuits. NPJ Syst. boil. Appl. 4: 40 PDF
GeneEx R Package (GitHub):
